///*
// *                    BioJava development code
// *
// * This code may be freely distributed and modified under the
// * terms of the GNU Lesser General Public Licence.  This should
// * be distributed with the code.  If you do not have a copy,
// * see:
// *
// *      http://www.gnu.org/copyleft/lesser.html
// *
// * Copyright for this code is held jointly by the individual
// * authors.  These should be listed in @author doc comments.
// *
// * For more information on the BioJava project and its aims,
// * or to join the biojava-l mailing list, visit the home page
// * at:
// *
// *      http://www.biojava.org/
// *
// * Created on June 7, 2010
// * Author: Mark Chapman
// */
//
//package org.jscc.app.client.biojava3.alignment.template;
//
//import java.util.concurrent.Future;
//import javax.swing.tree.TreeNode;
//
//import org.jscc.app.client.biojava3.core.sequence.template.Compound;
//import org.jscc.app.client.biojava3.core.sequence.template.Sequence;
//
///**
// * Defines a data structure for the node in a guide tree used during progressive multiple sequence alignment.
// * 
// * @author Mark Chapman
// * @param <S> each {@link Sequence} in the tree is of type S
// * @param <C> each element of a {@link Sequence} is a {@link Compound} of type C
// */
//public interface GuideTreeNode<S extends Sequence<C>, C extends Compound> extends TreeNode {
//
//    /**
//     * Returns the first child node of this node.  For leaf nodes (sequences), this will be null.
//     *
//     * @return the first child node of this node
//     */
//    GuideTreeNode<S, C> getChild1();
//
//    /**
//     * Returns the second child node of this node.  For leaf nodes (sequences), this will be null.
//     *
//     * @return the second child node of this node
//     */
//    GuideTreeNode<S, C> getChild2();
//
//    /**
//     * Returns the difference in height of this node and it's parent node.  A likely meaning of this distance is half
//     * the percent difference between this node and it's sibling node.
//     *
//     * @return the difference in height of this node to it's parent node
//     */
//    double getDistanceToParent();
//
//    /**
//     * Returns the name of this node.  For leaf nodes (sequences), this will likely be the accession ID.
//     *
//     * @return the name of this node
//     */
//    String getName();
//
//    /**
//     * Returns the profile stored at this node.  If the node is a leaf, the profile is that of a single sequence.  If
//     * not, this returns null until {@link #setProfile(Profile)} has been called.
//     *
//     * @return the profile stored at this node
//     */
//    Profile<S, C> getProfile();
//
//    /**
//     * Returns the profile future stored at this node, but does not force the calculation, yet.  This allows alignment
//     * tasks for the entire tree to be queued in a post-order traversal before concurrent execution.
//     *
//     * @return the profile future stored at this node
//     */
//    Future<ProfilePair<S, C>> getProfileFuture();
//
//    /**
//     * Stores the given profile.
//     *
//     * @param profile new profile stored at this node
//     */
//    void setProfile(Profile<S, C> profile);
//
//    /**
//     * Stores the given profile future.  This allows concurrent execution of alignment tasks.
//     *
//     * @param profile new profile to be calculated and then stored at this node
//     */
//    void setProfileFuture(Future<ProfilePair<S, C>> profileFuture);
//
//}
